gmx energy¶
Synopsis¶
gmx energy [-f [<.edr>]] [-f2 [<.edr>]] [-s [<.tpr>]] [-o [<.xvg>]]
[-viol [<.xvg>]] [-pairs [<.xvg>]] [-corr [<.xvg>]]
[-vis [<.xvg>]] [-evisco [<.xvg>]] [-eviscoi [<.xvg>]]
[-ravg [<.xvg>]] [-odh [<.xvg>]] [-b <time>] [-e <time>]
[-[no]w] [-xvg <enum>] [-[no]fee] [-fetemp <real>]
[-zero <real>] [-[no]sum] [-[no]dp] [-nbmin <int>]
[-nbmax <int>] [-[no]mutot] [-skip <int>] [-[no]aver]
[-nmol <int>] [-[no]fluct_props] [-[no]driftcorr]
[-[no]fluc] [-[no]orinst] [-[no]ovec] [-acflen <int>]
[-[no]normalize] [-P <enum>] [-fitfn <enum>]
[-beginfit <real>] [-endfit <real>]
Description¶
gmx energy extracts energy components
from an energy file. The user is prompted to interactively
select the desired energy terms.
Average, RMSD, and drift are calculated with full precision from the
simulation (see printed manual). Drift is calculated by performing
a least-squares fit of the data to a straight line. The reported total drift
is the difference of the fit at the first and last point.
An error estimate of the average is given based on a block averages
over 5 blocks using the full-precision averages. The error estimate
can be performed over multiple block lengths with the options
-nbmin and -nbmax.
Note that in most cases the energy files contains averages over all
MD steps, or over many more points than the number of frames in
energy file. This makes the gmx energy statistics output more accurate
than the .xvg output. When exact averages are not present in the energy
file, the statistics mentioned above are simply over the single, per-frame
energy values.
The term fluctuation gives the RMSD around the least-squares fit.
Some fluctuation-dependent properties can be calculated provided
the correct energy terms are selected, and that the command line option
-fluct_props is given. The following properties
will be computed:
| Property | Energy terms needed |
|---|---|
| Heat capacity C_p (NPT sims): | Enthalpy, Temp |
| Heat capacity C_v (NVT sims): | Etot, Temp |
| Thermal expansion coeff. (NPT): | Enthalpy, Vol, Temp |
| Isothermal compressibility: | Vol, Temp |
| Adiabatic bulk modulus: | Vol, Temp |
You always need to set the number of molecules -nmol.
The C_p/C_v computations do not include any corrections
for quantum effects. Use the gmx dos program if you need that (and you do).
Option -odh extracts and plots the free energy data
(Hamiltoian differences and/or the Hamiltonian derivative dhdl)
from the ener.edr file.
With -fee an estimate is calculated for the free-energy
difference with an ideal gas state:
Delta A = A(N,V,T) - A_idealgas(N,V,T) = kT ln(<exp(U_pot/kT)>)
Delta G = G(N,p,T) - G_idealgas(N,p,T) = kT ln(<exp(U_pot/kT)>)
where k is Boltzmann’s constant, T is set by -fetemp and
the average is over the ensemble (or time in a trajectory).
Note that this is in principle
only correct when averaging over the whole (Boltzmann) ensemble
and using the potential energy. This also allows for an entropy
estimate using:
Delta S(N,V,T) = S(N,V,T) - S_idealgas(N,V,T) = (<U_pot> - Delta A)/T
Delta S(N,p,T) = S(N,p,T) - S_idealgas(N,p,T) = (<U_pot> + pV - Delta G)/T
When a second energy file is specified (-f2), a free energy
difference is calculated:
dF = -kT ln(<exp(-(E_B-E_A)/kT)>_A) ,
where E_A and E_B are the energies from the first and second energy
files, and the average is over the ensemble A. The running average
of the free energy difference is printed to a file specified by -ravg.
Note that the energies must both be calculated from the same trajectory.
Options¶
Options to specify input files:
-f[<.edr>] (ener.edr)- Energy file
-f2[<.edr>] (ener.edr) (Optional)- Energy file
-s[<.tpr>] (topol.tpr) (Optional)- Portable xdr run input file
Options to specify output files:
-o[<.xvg>] (energy.xvg)- xvgr/xmgr file
-viol[<.xvg>] (violaver.xvg) (Optional)- xvgr/xmgr file
-pairs[<.xvg>] (pairs.xvg) (Optional)- xvgr/xmgr file
-corr[<.xvg>] (enecorr.xvg) (Optional)- xvgr/xmgr file
-vis[<.xvg>] (visco.xvg) (Optional)- xvgr/xmgr file
-evisco[<.xvg>] (evisco.xvg) (Optional)- xvgr/xmgr file
-eviscoi[<.xvg>] (eviscoi.xvg) (Optional)- xvgr/xmgr file
-ravg[<.xvg>] (runavgdf.xvg) (Optional)- xvgr/xmgr file
-odh[<.xvg>] (dhdl.xvg) (Optional)- xvgr/xmgr file
Other options:
-b<time> (0)- Time of first frame to read from trajectory (default unit ps)
-e<time> (0)- Time of last frame to read from trajectory (default unit ps)
-[no]w(no)- View output .xvg, .xpm, .eps and .pdb files
-xvg<enum> (xmgrace)- xvg plot formatting: xmgrace, xmgr, none
-[no]fee(no)- Do a free energy estimate
-fetemp<real> (300)- Reference temperature for free energy calculation
-zero<real> (0)- Subtract a zero-point energy
-[no]sum(no)- Sum the energy terms selected rather than display them all
-[no]dp(no)- Print energies in high precision
-nbmin<int> (5)- Minimum number of blocks for error estimate
-nbmax<int> (5)- Maximum number of blocks for error estimate
-[no]mutot(no)- Compute the total dipole moment from the components
-skip<int> (0)- Skip number of frames between data points
-[no]aver(no)- Also print the exact average and rmsd stored in the energy frames (only when 1 term is requested)
-nmol<int> (1)- Number of molecules in your sample: the energies are divided by this number
-[no]fluct_props(no)- Compute properties based on energy fluctuations, like heat capacity
-[no]driftcorr(no)- Useful only for calculations of fluctuation properties. The drift in the observables will be subtracted before computing the fluctuation properties.
-[no]fluc(no)- Calculate autocorrelation of energy fluctuations rather than energy itself
-[no]orinst(no)- Analyse instantaneous orientation data
-[no]ovec(no)- Also plot the eigenvectors with
-oten -acflen<int> (-1)- Length of the ACF, default is half the number of frames
-[no]normalize(yes)- Normalize ACF
-P<enum> (0)- Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
-fitfn<enum> (none)- Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
-beginfit<real> (0)- Time where to begin the exponential fit of the correlation function
-endfit<real> (-1)- Time where to end the exponential fit of the correlation function, -1 is until the end